Hi Tommy, There is nothing in ChimeraX to automatically do all the steps of this for you, i.e. figure out how to position the protein in the lipid membrane, place it there, and adjust the lipid molecules so that they are not in the way. There may be web servers that do this whole process if CHARMM-GUI does not, but I have no specific knowledge. You could try "googling it" or using some other web search method. Limited parts of this process could be done in ChimeraX: If you already have some good idea of how the protein is positioned relative to the membrane, you could manually move it there, and then remove all the lipid molecules within some close distance of the protein atoms to get rid of the clashes/intersections. How to move one or more models while others remain frozen in place (selective manipulation): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> Then you could delete residues in the membrane that are within some distance of atoms in the protein. I can't give a specific command since I don't what models/chains/residues you have that contain the protein and the lipid membrane, but there is a "delete" command and ways to specify atoms within some zone of other atoms in the command line, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/delete.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones> ... or you could use the menu, namely Select... Zone and then to delete the selected atoms, Actions... Atoms/Bonds... Delete. <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions> How careful you would need to be depends on what you plan to do next with this composite structure. If you were going to use it as input to some other simulation program, those subsequent steps may help to relieve minor clashes (although you still wouldn't want molecules completely on top of each other). If you don't know how the protein might sit relative to the membrane, maybe you can use the OPM server to predict that. However, it just draws boundaries with dummy atoms and would not place the protein in a full atomic bilayer. You'd still have to do that yourself somehow. I hope this helps, Elaine ---- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 12, 2025, at 4:11 PM, Tommy Tong via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX experts, Good afternoon. My name is Tommy from San Diego Biomed. I am a beginner to ChimeraX version 1.9. May I ask if it is possible to use ChimeraX to dock a membrane protein into a lipid bilayer? I obtained Phosphotidylcholine bilayer (POPC) structure from CHARMM-GUI webpage https://charmm-gui.org/?doc=archive&lib=lipid_pure, and was wondering if it is possible to “place” a protein into this POPC structure in ChimeraX. Your help and advice on this is greatly appreciated. Thank you. Sincerely, Tommy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/